I am trying to setup Eclipse (Kepler SR2) to work with web-based projects (PHP, HTML, JavaScript). using Web Development Tools, PHP Development Tools and Remote System Explorer, as alternative to Aptana (because of it's bundeled PyDev version lag).

Now, when I want to start syncing local files to web server, I select "Export from project.." option in "Remote System Explorer" Perspective on remote target directory, check Review/Sync option, and in result, after "Put" action in "Team Synchronizing" perspective I get in result that all selected files are exported into subdirectory named "My Project Name".

As specific example, I've got project with some subdirs (It's for custom Drupal modules which has to be uploaded into specific website subdirectory):